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| November 2015 Volume 47, Issue 11 |  | | |  |  Editorial
News and Views
Analysis
Brief Communication
Articles
Letters | | | Advertisement | | | |  Announcing new solutions for SNP Genotyping using PCR and HRM
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| | | | | | Advertisement | | Nature Plants: Call for Papers
Nature Plants launched in January and covers all aspects of plants be it their evolution, genetics, development or metabolism, their interactions with the environment, or their societal significance. The journal welcomes high quality submissions and encourages you and your colleagues to consider submitting your next research paper to the journal.
Submit your next research paper to the journal. | | | | | | | Editorial |  Top | |  | | A new genomic island p1221
doi:10.1038/ng.3436
A large collection of human genomes from Sardinia is reported in three linked papers that implicate new genetic variants in the regulation of height, blood lipids, inflammatory markers and hemoglobin levels. These analyses provide new insight into disease susceptibility and evolution in isolated human populations and illuminate the genetics of complex phenotypes. | | News and Views | Top | | | | | | Analysis | Top | | | | Partitioning heritability by functional annotation using genome-wide association summary statistics pp1228 - 1235
Hilary K Finucane, Brendan Bulik-Sullivan, Alexander Gusev, Gosia Trynka, Yakir Reshef, Po-Ru Loh, Verneri Anttila, Han Xu, Chongzhi Zang, Kyle Farh, Stephan Ripke, Felix R Day, ReproGen Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, The RACI Consortium, Shaun Purcell, Eli Stahl, Sara Lindstrom, John R B Perry, Yukinori Okada, Soumya Raychaudhuri, Mark J Daly, Nick Patterson, Benjamin M Neale & Alkes L Price
doi:10.1038/ng.3404
Hilary Finucane, Brendan Bulik-Sullivan, Benjamin Neale, Alkes Price and colleagues introduce a new method, called stratified LD score regression, for partitioning heritability by functional category using genome-wide association study summary statistics. They observe a substantial enrichment of heritability in conserved regions and illustrate how this approach can provide insights into the biological basis of disease and direction for functional follow-up. | | | | An atlas of genetic correlations across human diseases and traits pp1236 - 1241
Brendan Bulik-Sullivan, Hilary K Finucane, Verneri Anttila, Alexander Gusev, Felix R Day, Po-Ru Loh, ReproGen Consortium, Psychiatric Genomics Consortium, Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium 3, Laramie Duncan, John R B Perry, Nick Patterson, Elise B Robinson, Mark J Daly, Alkes L Price & Benjamin M Neale
doi:10.1038/ng.3406
Brendan Bulik-Sullivan, Benjamin Neale, Hilary Finucane, Alkes Price and colleagues introduce a new technique for estimating genetic correlation that requires only genome-wide association summary statistics and that is not biased by sample overlap. Using this method, they find genetic correlations between anorexia nervosa and schizophrenia, and between educational attainment and autism spectrum disorder. | | | | Intron retention is a widespread mechanism of tumor-suppressor inactivation pp1242 - 1248
Hyunchul Jung, Donghoon Lee, Jongkeun Lee, Donghyun Park, Yeon Jeong Kim, Woong-Yang Park, Dongwan Hong, Peter J Park & Eunjung Lee
doi:10.1038/ng.3414
Eunjung Lee, Peter Park, Dongwan Hong and colleagues report an analysis of cancer RNA sequencing data identifying approximately 900 somatic coding variants that cause disrupted splicing in cancer, leading to intron retention or exon skipping in many cases. Variants causing intron retention are enriched for loss-of-function mutations in tumor-suppressor genes. | | | | Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation pp1249 - 1259
Alvaro J González, Manu Setty & Christina S Leslie
doi:10.1038/ng.3402
Christina Leslie and colleagues report an integrative analysis of the enhancer landscape and gene expression dynamics during hematopoietic differentiation. They also develop a quantitative model to predict gene expression changes from DNA sequence content and the lineage history of active enhancers and suggest a new mechanistic role for PU.1 at transition peaks during B cell specification. | | Brief Communication | Top | | | | MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates pp1260 - 1263
Anne Guimier, George C Gabriel, Fanny Bajolle, Michael Tsang, Hui Liu, Aaron Noll, Molly Schwartz, Rajae El Malti, Laurie D Smith, Nikolai T Klena, Gina Jimenez, Neil A Miller, Myriam Oufadem, Anne Moreau de Bellaing, Hisato Yagi, Carol J Saunders, Candice N Baker, Sylvie Di Filippo, Kevin A Peterson, Isabelle Thiffault, Christine Bole-Feysot, Linda D Cooley, Emily G Farrow, Cécile Masson, Patric Schoen, Jean-François Deleuze, Patrick Nitschké, Stanislas Lyonnet, Loic de Pontual, Stephen A Murray, Damien Bonnet, Stephen F Kingsmore, Jeanne Amiel, Patrice Bouvagnet, Cecilia W Lo & Christopher T Gordon
doi:10.1038/ng.3376
Christopher Gordon, Cecilia Lo, Patrice Bouvagnet and colleagues report loss-of-function mutations in the MMP21 gene (encoding matrix metallopeptidase 21) that cause human heterotaxy with associated complex congenital heart defects. The authors confirm the role of MMP21 in heterotaxy and left-right patterning in zebrafish and mouse models.
See also: News and Views by Vissers & Veltman | Letter by Akawi et al. | | | Advertisement | | | | | | | Articles | Top | | | | Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels pp1264 - 1271
Fabrice Danjou, Magdalena Zoledziewska, Carlo Sidore, Maristella Steri, Fabio Busonero, Andrea Maschio, Antonella Mulas, Lucia Perseu, Susanna Barella, Eleonora Porcu, Giorgio Pistis, Maristella Pitzalis, Mauro Pala, Stephan Menzel, Sarah Metrustry, Timothy D Spector, Lidia Leoni, Andrea Angius, Manuela Uda, Paolo Moi, Swee Lay Thein, Renzo Galanello, Gonçalo R Abecasis, David Schlessinger, Serena Sanna & Francesco Cucca
doi:10.1038/ng.3307
Francesco Cucca, Serena Sanna, David Schlessinger, Goncalo Abecasis and colleagues report genome-wide association analysis results for the levels of A1, A2 and fetal hemoglobin in a large Sardinian cohort. By integrating high-density array genotyping and whole-genome sequencing, they detect 23 associations at 10 loci and observe a wide range of pleiotropic effects of variants across the 3 hemoglobin types.
See also: News and Views by Lettre & Hirschhorn | Article by Sidore et al. | Letter by Zoledziewska et al. | | | | Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers pp1272 - 1281
Carlo Sidore, Fabio Busonero, Andrea Maschio, Eleonora Porcu, Silvia Naitza, Magdalena Zoledziewska, Antonella Mulas, Giorgio Pistis, Maristella Steri, Fabrice Danjou, Alan Kwong, Vicente Diego Ortega del Vecchyo, Charleston W K Chiang, Jennifer Bragg-Gresham, Maristella Pitzalis, Ramaiah Nagaraja, Brendan Tarrier, Christine Brennan, Sergio Uzzau, Christian Fuchsberger, Rossano Atzeni, Frederic Reinier, Riccardo Berutti, Jie Huang, Nicholas J Timpson, Daniela Toniolo, Paolo Gasparini, Giovanni Malerba, George Dedoussis, Eleftheria Zeggini, Nicole Soranzo, Chris Jones, Robert Lyons, Andrea Angius, Hyun M Kang, John Novembre, Serena Sanna, David Schlessinger, Francesco Cucca & Gonçalo R Abecasis
doi:10.1038/ng.3368
Gonçalo Abecasis, Francesco Cucca, David Schlessinger, Serena Sanna and colleagues report ~17.6 million genetic variants from whole-genome sequencing of 2,120 Sardinians. They assess the impact of these variants on circulating lipid levels and five inflammatory biomarkers.
See also: News and Views by Lettre & Hirschhorn | Article by Danjou et al. | Letter by Zoledziewska et al. | | | | Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation pp1282 - 1293
Norihiro Kato, Marie Loh, Fumihiko Takeuchi, Niek Verweij, Xu Wang, Weihua Zhang, Tanika N Kelly, Danish Saleheen, Benjamin Lehne, Irene Mateo Leach, Alexander W Drong, James Abbott, Simone Wahl, Sian-Tsung Tan, William R Scott, Gianluca Campanella, Marc Chadeau-Hyam, Uzma Afzal, Tarunveer S Ahluwalia, Marc Jan Bonder, Peng Chen, Abbas Dehghan, Todd L Edwards, Tõnu Esko, Min Jin Go, Sarah E Harris, Jaana Hartiala, Silva Kasela, Anuradhani Kasturiratne, Chiea-Chuen Khor, Marcus E Kleber, Huaixing Li, Zuan Yu Mok, Masahiro Nakatochi, Nur Sabrina Sapari, Richa Saxena, Alexandre F R Stewart, Lisette Stolk, Yasuharu Tabara, Ai Ling Teh, Ying Wu, Jer-Yuarn Wu, Yi Zhang, Imke Aits, Alexessander Da Silva Couto Alves, Shikta Das, Rajkumar Dorajoo, Jemma C Hopewell, Yun Kyoung Kim, Robert W Koivula, Jian'an Luan, Leo-Pekka Lyytikäinen, Quang N Nguyen, Mark A Pereira, Iris Postmus, Olli T Raitakari, Molly Scannell Bryan, Robert A Scott, Rossella Sorice, Vinicius Tragante, Michela Traglia, Jon White, Ken Yamamoto, Yonghong Zhang, Linda S Adair, Alauddin Ahmed, Koichi Akiyama, Rasheed Asif, Tin Aung, Inês Barroso, Andrew Bjonnes, Timothy R Braun, Hui Cai, Li-Ching Chang, Chien-Hsiun Chen, Ching-Yu Cheng, Yap-Seng Chong, Rory Collins, Regina Courtney, Gail Davies, Graciela Delgado, Loi D Do, Pieter A Doevendans, Ron T Gansevoort, Yu-Tang Gao, Tanja B Grammer, Niels Grarup, Jagvir Grewal, Dongfeng Gu, Gurpreet S Wander, Anna-Liisa Hartikainen, Stanley L Hazen, Jing He, Chew-Kiat Heng, James E Hixson, Albert Hofman, Chris Hsu, Wei Huang, Lise L N Husemoen, Joo-Yeon Hwang, Sahoko Ichihara, Michiya Igase, Masato Isono, Johanne M Justesen, Tomohiro Katsuya, Muhammad G Kibriya, Young Jin Kim, Miyako Kishimoto, Woon-Puay Koh, Katsuhiko Kohara, Meena Kumari, Kenneth Kwek, Nanette R Lee, Jeannette Lee, Jiemin Liao, Wolfgang Lieb, David C M Liewald, Tatsuaki Matsubara, Yumi Matsushita, Thomas Meitinger, Evelin Mihailov, Lili Milani, Rebecca Mills, Nina Mononen, Martina Müller-Nurasyid, Toru Nabika, Eitaro Nakashima, Hong Kiat Ng, Kjell Nikus, Teresa Nutile, Takayoshi Ohkubo, Keizo Ohnaka, Sarah Parish, Lavinia Paternoster, Hao Peng, Annette Peters, Son T Pham, Mohitha J Pinidiyapathirage, Mahfuzar Rahman, Hiromi Rakugi, Olov Rolandsson, Michelle Ann Rozario, Daniela Ruggiero, Cinzia F Sala, Ralhan Sarju, Kazuro Shimokawa, Harold Snieder, Thomas Sparsø, Wilko Spiering, John M Starr, David J Stott, Daniel O Stram, Takao Sugiyama, Silke Szymczak, W H Wilson Tang, Lin Tong, Stella Trompet, Väinö Turjanmaa, Hirotsugu Ueshima, André G Uitterlinden, Satoshi Umemura, Marja Vaarasmaki, Rob M van Dam, Wiek H van Gilst, Dirk J van Veldhuisen, Jorma S Viikari, Melanie Waldenberger, Yiqin Wang, Aili Wang, Rory Wilson, Tien-Yin Wong, Yong-Bing Xiang, Shuhei Yamaguchi, Xingwang Ye, Robin D Young, Terri L Young, Jian-Min Yuan, Xueya Zhou, Folkert W Asselbergs, Marina Ciullo, Robert Clarke, Panos Deloukas, Andre Franke, Paul W Franks, Steve Franks, Yechiel Friedlander, Myron D Gross, Zhirong Guo, Torben Hansen, Marjo-Riitta Jarvelin, Torben Jørgensen, J Wouter Jukema, Mika Kähönen, Hiroshi Kajio, Mika Kivimaki, Jong-Young Lee, Terho Lehtimäki, Allan Linneberg, Tetsuro Miki, Oluf Pedersen, Nilesh J Samani, Thorkild I A Sørensen, Ryoichi Takayanagi, Daniela Toniolo, BIOS-consortium, CARDIo GRAMplusCD, LifeLines Cohort Study, The InterAct Consortium, Habibul Ahsan, Hooman Allayee, Yuan-Tsong Chen, John Danesh, Ian J Deary, Oscar H Franco, Lude Franke, Bastiaan T Heijman, Joanna D Holbrook, Aaron Isaacs, Bong-Jo Kim, Xu Lin, Jianjun Liu, Winfried März, Andres Metspalu, Karen L Mohlke, Dharambir K Sanghera, Xiao-Ou Shu, Joyce B J van Meurs, Eranga Vithana, Ananda R Wickremasinghe, Cisca Wijmenga, Bruce H W Wolffenbuttel, Mitsuhiro Yokota, Wei Zheng, Dingliang Zhu, Paolo Vineis, Soterios A Kyrtopoulos, Jos C S Kleinjans, Mark I McCarthy, Richie Soong, Christian Gieger, James Scott, Yik-Ying Teo, Jiang He, Paul Elliott, E Shyong Tai, Pim van der Harst, Jaspal S Kooner & John C Chambers
doi:10.1038/ng.3405
John Chambers, Jaspal Kooner, Pim van der Harst, Shyong Tai, Paul Elliott, Jiang He, Norihiro Kato and colleagues performed a genome-wide association study of blood pressure phenotypes in individuals of European, East Asian and South Asian ancestry. They find trait-associated SNPs at 12 loci, some of which are associated with methylation at nearby CpG sites. | | | | Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair pp1294 - 1303
Felix R Day, Katherine S Ruth, Deborah J Thompson, Kathryn L Lunetta, Natalia Pervjakova, Daniel I Chasman, Lisette Stolk, Hilary K Finucane, Patrick Sulem, Brendan Bulik-Sullivan, Tõnu Esko, Andrew D Johnson, Cathy E Elks, Nora Franceschini, Chunyan He, Elisabeth Altmaier, Jennifer A Brody, Lude L Franke, Jennifer E Huffman, Margaux F Keller, Patrick F McArdle, Teresa Nutile, Eleonora Porcu, Antonietta Robino, Lynda M Rose, Ursula M Schick, Jennifer A Smith, Alexander Teumer, Michela Traglia, Dragana Vuckovic, Jie Yao, Wei Zhao, Eva Albrecht, Najaf Amin, Tanguy Corre, Jouke-Jan Hottenga, Massimo Mangino, Albert V Smith, Toshiko Tanaka, Gonçalo R Abecasis, Irene L Andrulis, Hoda Anton-Culver, Antonis C Antoniou, Volker Arndt, Alice M Arnold, Caterina Barbieri, Matthias W Beckmann, Alicia Beeghly-Fadiel, Javier Benitez, Leslie Bernstein, Suzette J Bielinski, Carl Blomqvist, Eric Boerwinkle, Natalia V Bogdanova, Stig E Bojesen, Manjeet K Bolla, Anne-Lise Borresen-Dale, Thibaud S Boutin, Hiltrud Brauch, Hermann Brenner, Thomas Brüning, Barbara Burwinkel, Archie Campbell, Harry Campbell, Stephen J Chanock, J Ross Chapman, Yii-Der Ida Chen, Georgia Chenevix-Trench, Fergus J Couch, Andrea D Coviello, Angela Cox, Kamila Czene, Hatef Darabi, Immaculata De Vivo, Ellen W Demerath, Joe Dennis, Peter Devilee, Thilo Dörk, Isabel dos-Santos-Silva, Alison M Dunning, John D Eicher, Peter A Fasching, Jessica D Faul, Jonine Figueroa, Dieter Flesch-Janys, Ilaria Gandin, Melissa E Garcia, Montserrat García-Closas, Graham G Giles, Giorgia G Girotto, Mark S Goldberg, Anna González-Neira, Mark O Goodarzi, Megan L Grove, Daniel F Gudbjartsson, Pascal Guénel, Xiuqing Guo, Christopher A Haiman, Per Hall, Ute Hamann, Brian E Henderson, Lynne J Hocking, Albert Hofman, Georg Homuth, Maartje J Hooning, John L Hopper, Frank B Hu, Jinyan Huang, Keith Humphreys, David J Hunter, Anna Jakubowska, Samuel E Jones, Maria Kabisch, David Karasik, Julia A Knight, Ivana Kolcic, Charles Kooperberg, Veli-Matti Kosma, Jennifer Kriebel, Vessela Kristensen, Diether Lambrechts, Claudia Langenberg, Jingmei Li, Xin Li, Sara Lindström, Yongmei Liu, Jian'an Luan, Jan Lubinski, Reedik Mägi, Arto Mannermaa, Judith Manz, Sara Margolin, Jonathan Marten, Nicholas G Martin, Corrado Masciullo, Alfons Meindl, Kyriaki Michailidou, Evelin Mihailov, Lili Milani, Roger L Milne, Martina Müller-Nurasyid, Michael Nalls, Benjamin M Neale, Heli Nevanlinna, Patrick Neven, Anne B Newman, Børge G Nordestgaard, Janet E Olson, Sandosh Padmanabhan, Paolo Peterlongo, Ulrike Peters, Astrid Petersmann, Julian Peto, Paul D P Pharoah, Nicola N Pirastu, Ailith Pirie, Giorgio Pistis, Ozren Polasek, David Porteous, Bruce M Psaty, Katri Pylkäs, Paolo Radice, Leslie J Raffel, Fernando Rivadeneira, Igor Rudan, Anja Rudolph, Daniela Ruggiero, Cinzia F Sala, Serena Sanna, Elinor J Sawyer, David Schlessinger, Marjanka K Schmidt, Frank Schmidt, Rita K Schmutzler, Minouk J Schoemaker, Robert A Scott, Caroline M Seynaeve, Jacques Simard, Rossella Sorice, Melissa C Southey, Doris Stöckl, Konstantin Strauch, Anthony Swerdlow, Kent D Taylor, Unnur Thorsteinsdottir, Amanda E Toland, Ian Tomlinson, Thérèse Truong, Laufey Tryggvadottir, Stephen T Turner, Diego Vozzi, Qin Wang, Melissa Wellons, Gonneke Willemsen, James F Wilson, Robert Winqvist, Bruce B H R Wolffenbuttel, Alan F Wright, Drakoulis Yannoukakos, Tatijana Zemunik, Wei Zheng, Marek Zygmunt, Sven Bergmann, Dorret I Boomsma, Julie E Buring, Luigi Ferrucci, Grant W Montgomery, Vilmundur Gudnason, Tim D Spector, Cornelia M van Duijn, Behrooz Z Alizadeh, Marina Ciullo, Laura Crisponi, Douglas F Easton, Paolo P Gasparini, Christian Gieger, Tamara B Harris, Caroline Hayward, Sharon L R Kardia, Peter Kraft, Barbara McKnight, Andres Metspalu, Alanna C Morrison, Alex P Reiner, Paul M Ridker, Jerome I Rotter, Daniela Toniolo, André G Uitterlinden, Sheila Ulivi, Henry Völzke, Nicholas J Wareham, David R Weir, Laura M Yerges-Armstrong, The PRACTICAL Consortium, kConFab Investigators, AOCS Investigators, Generation Scotland, EPIC-InterAct Consortium, LifeLines Cohort Study, Alkes L Price, Kari Stefansson, Jenny A Visser, Ken K Ong, Jenny Chang-Claude, Joanne M Murabito, John R B Perry & Anna Murray
doi:10.1038/ng.3412
John Perry and colleagues report the results of a large genome-wide association study meta-analysis to identify variants influencing age at natural menopause. They identify 54 independent signals and find enrichment near genes involved in delayed puberty and DNA damage response. | | | | Integrated molecular analysis of adult T cell leukemia/lymphoma pp1304 - 1315
Keisuke Kataoka, Yasunobu Nagata, Akira Kitanaka, Yuichi Shiraishi, Teppei Shimamura, Jun-ichirou Yasunaga, Yasushi Totoki, Kenichi Chiba, Aiko Sato-Otsubo, Genta Nagae, Ryohei Ishii, Satsuki Muto, Shinichi Kotani, Yosaku Watatani, June Takeda, Masashi Sanada, Hiroko Tanaka, Hiromichi Suzuki, Yusuke Sato, Yusuke Shiozawa, Tetsuichi Yoshizato, Kenichi Yoshida, Hideki Makishima, Masako Iwanaga, Guangyong Ma, Kisato Nosaka, Masakatsu Hishizawa, Hidehiro Itonaga, Yoshitaka Imaizumi, Wataru Munakata, Hideaki Ogasawara, Toshitaka Sato, Ken Sasai, Kenzo Muramoto, Marina Penova, Takahisa Kawaguchi, Hiromi Nakamura, Natsuko Hama, Kotaro Shide, Yoko Kubuki, Tomonori Hidaka, Takuro Kameda, Tsuyoshi Nakamaki, Ken Ishiyama, Shuichi Miyawaki, Sung-Soo Yoon, Kensei Tobinai, Yasushi Miyazaki, Akifumi Takaori-Kondo, Fumihiko Matsuda, Kengo Takeuchi, Osamu Nureki, Hiroyuki Aburatani, Toshiki Watanabe, Tatsuhiro Shibata, Masao Matsuoka, Satoru Miyano, Kazuya Shimoda & Seishi Ogawa
doi:10.1038/ng.3415
Seishi Ogawa and colleagues report the results of a large-scale sequencing study of adult T cell leukemia/lymphoma. They find recurrent alterations enriched for T cell receptor/NF-κB signaling, T cell trafficking and other T cell pathways and highlight targets for the development of new therapeutics for this intractable cancer.
See also: News and Views by Vicente & Cools | | | | DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control pp1316 - 1325
Helene Kretzmer, Stephan H Bernhart, Wei Wang, Andrea Haake, Marc A Weniger, Anke K Bergmann, Matthew J Betts, Enrique Carrillo-de-Santa-Pau, Gero Doose, Jana Gutwein, Julia Richter, Volker Hovestadt, Bingding Huang, Daniel Rico, Frank Jühling, Julia Kolarova, Qianhao Lu, Christian Otto, Rabea Wagener, Judith Arnolds, Birgit Burkhardt, Alexander Claviez, Hans G Drexler, Sonja Eberth, Roland Eils, Paul Flicek, Siegfried Haas, Michael Hummel, Dennis Karsch, Hinrik H D Kerstens, Wolfram Klapper, Markus Kreuz, Chris Lawerenz, Dido Lenze, Markus Loeffler, Cristina López, Roderick A F MacLeod, Joost H A Martens, Marta Kulis, José Ignacio Martín-Subero, Peter Möller, Inga Nagel, Simone Picelli, Inga Vater, Marius Rohde, Philip Rosenstiel, Maciej Rosolowski, Robert B Russell, Markus Schilhabel, Matthias Schlesner, Peter F Stadler, Monika Szczepanowski, Lorenz Trümper, Hendrik G Stunnenberg, ICGC MMML-Seq project, BLUEPRINT project, Ralf Küppers, Ole Ammerpohl, Peter Lichter, Reiner Siebert, Steve Hoffmann & Bernhard Radlwimmer
doi:10.1038/ng.3413
Bernhard Radlwimmer and colleagues report whole-genome bisulfite sequencing of 13 Burkitt lymphomas and nine follicular lymphomas. They find that both types of germinal center B cell lymphomas show global hypomethylation compared to normal germinal center B cell precursors and identify regions of differential methylation that correlate with somatic mutations and differential gene expression. | | | | The genomic landscape of juvenile myelomonocytic leukemia pp1326 - 1333
Elliot Stieglitz, Amaro N Taylor-Weiner, Tiffany Y Chang, Laura C Gelston, Yong-Dong Wang, Tali Mazor, Emilio Esquivel, Ariel Yu, Sara Seepo, Scott R Olsen, Mara Rosenberg, Sophie L Archambeault, Ghada Abusin, Kyle Beckman, Patrick A Brown, Michael Briones, Benjamin Carcamo, Todd Cooper, Gary V Dahl, Peter D Emanuel, Mark N Fluchel, Rakesh K Goyal, Robert J Hayashi, Johann Hitzler, Christopher Hugge, Y Lucy Liu, Yoav H Messinger, Donald H Mahoney Jr, Philip Monteleone, Eneida R Nemecek, Philip A Roehrs, Reuven J Schore, Kimo C Stine, Clifford M Takemoto, Jeffrey A Toretsky, Joseph F Costello, Adam B Olshen, Chip Stewart, Yongjin Li, Jing Ma, Robert B Gerbing, Todd A Alonzo, Gad Getz, Tanja A Gruber, Todd R Golub, Kimberly Stegmaier & Mignon L Loh
doi:10.1038/ng.3400
Elliot Stieglitz, Mignon Loh and colleagues report the whole-exome sequencing of diagnostic and relapsed samples from patients with juvenile myelomonocytic leukemia. They identify new recurrent mutations for this disease and find that the number of somatic alterations present at diagnosis may be predictive of clinical outcome. | | | Advertisement | | Presented by The Chinese Academy of Agricultural Sciences, Chinese Academy of Sciences, Fujian Agriculture and Forestry University, and Nature Genetics
AGRICULTURAL GENOMICS 2015 — FROM VARIATION TO IMPROVED PRODUCTION November 16-18, 2015| Shenzhen, China |  | | | | | | Letters | Top | | | | Juvenile myelomonocytic leukemia displays mutations in components of the RAS pathway and the PRC2 network pp1334 - 1340
Aurélie Caye, Marion Strullu, Fabien Guidez, Bruno Cassinat, Steven Gazal, Odile Fenneteau, Elodie Lainey, Kazem Nouri, Saeideh Nakhaei-Rad, Radovan Dvorsky, Julie Lachenaud, Sabrina Pereira, Jocelyne Vivent, Emmanuelle Verger, Dominique Vidaud, Claire Galambrun, Capucine Picard, Arnaud Petit, Audrey Contet, Marilyne Poirée, Nicolas Sirvent, Françoise Méchinaud, Dalila Adjaoud, Catherine Paillard, Brigitte Nelken, Yves Reguerre, Yves Bertrand, Dieter Häussinger, Jean-Hugues Dalle, Mohammad Reza Ahmadian, André Baruchel, Christine Chomienne & Hélène Cavé
doi:10.1038/ng.3420
Hélène Cavé and colleagues genetically profile a cohort of 118 juvenile myelomonocytic leukemia (JMML) samples and uncover mutations in multiple components of the RAS signaling pathway and the PRC2 network. Their study demonstrates an association between JMML clinical outcome and mutational profile and suggests a dose-dependent effect for RAS pathway activation. | | | | Genomic landscapes of breast fibroepithelial tumors pp1341 - 1345
Jing Tan, Choon Kiat Ong, Weng Khong Lim, Cedric Chuan Young Ng, Aye Aye Thike, Ley Moy Ng, Vikneswari Rajasegaran, Swe Swe Myint, Sanjanaa Nagarajan, Saranya Thangaraju, Sucharita Dey, Nur Diyana Md Nasir, Giovani Claresta Wijaya, Jing Quan Lim, Dachuan Huang, Zhimei Li, Bernice Huimin Wong, Jason Yong Sheng Chan, John R McPherson, Ioana Cutcutache, Gregory Poore, Su Ting Tay, Wai Jin Tan, Thomas Choudary Putti, Buhari Shaik Ahmad, Philip Iau, Ching Wan Chan, Anthony P H Tang, Wei Sean Yong, Preetha Madhukumar, Gay Hui Ho, Veronique Kiak Mien Tan, Chow Yin Wong, Mikael Hartman, Kong Wee Ong, Benita K T Tan, Steven G Rozen, Patrick Tan, Puay Hoon Tan & Bin Tean Teh
doi:10.1038/ng.3409
Bin Tean Teh and colleagues report the genomic characterization of 100 breast fibroepithelial tumors, including benign fibroadenomas and benign, borderline and malignant phyllodes tumors. They identify mutations specific to phyllodes tumors and find somatic mutation patterns that distinguish borderline and malignant phyllodes tumors from the other tumor types. | | | | The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis pp1346 - 1351
Mark M Pomerantz, Fugen Li, David Y Takeda, Romina Lenci, Apurva Chonkar, Matthew Chabot, Paloma Cejas, Francisca Vazquez, Jennifer Cook, Ramesh A Shivdasani, Michaela Bowden, Rosina Lis, William C Hahn, Philip W Kantoff, Myles Brown, Massimo Loda, Henry W Long & Matthew L Freedman
doi:10.1038/ng.3419
Matthew Freedman and colleagues show that androgen receptor (AR) binding sites undergo extensive reprogramming during prostate epithelial transformation. They further show that FOXA1 and HOXB13 colocalize at reprogrammed AR binding sites in human tumor tissue and are able to reprogram the AR cistrome of an immortalized prostate cell line to resemble that of prostate tumors. | | | | Height-reducing variants and selection for short stature in Sardinia pp1352 - 1356
Magdalena Zoledziewska, Carlo Sidore, Charleston W K Chiang, Serena Sanna, Antonella Mulas, Maristella Steri, Fabio Busonero, Joseph H Marcus, Michele Marongiu, Andrea Maschio, Diego Ortega Del Vecchyo, Matteo Floris, Antonella Meloni, Alessandro Delitala, Maria Pina Concas, Federico Murgia, Ginevra Biino, Simona Vaccargiu, Ramaiah Nagaraja, Kirk E Lohmueller, UK10K Consortium, Nicholas J Timpson, Nicole Soranzo, Ioanna Tachmazidou, George Dedoussis, Eleftheria Zeggini, The Understanding Society Scientific Group, Sergio Uzzau, Chris Jones, Robert Lyons, Andrea Angius, Gonçalo R Abecasis, John Novembre, David Schlessinger & Francesco Cucca
doi:10.1038/ng.3403
Francesco Cucca, David Schlessinger, John Novembre, Goncalo Abecasis and colleagues present sequencing-based whole-genome association analyses for stature in Sardinia and identify two variants that lead to reduced height. Their findings suggest that shorter stature was selected for in Sardinia.
See also: News and Views by Lettre & Hirschhorn | Article by Danjou et al. | Article by Sidore et al. | | | | Population genetic differentiation of height and body mass index across Europe pp1357 - 1362
Matthew R Robinson, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, Anna Vinkhuyzen, Sonja I Berndt, Stefan Gustafsson, Anne E Justice, Bratati Kahali, Adam E Locke, Tune H Pers, Sailaja Vedantam, Andrew R Wood, Wouter van Rheenen, Ole A Andreassen, Paolo Gasparini, Andres Metspalu, Leonard H van den Berg, Jan H Veldink, Fernando Rivadeneira, Thomas M Werge, Goncalo R Abecasis, Dorret I Boomsma, Daniel I Chasman, Eco J C de Geus, Timothy M Frayling, Joel N Hirschhorn, Jouke Jan Hottenga, Erik Ingelsson, Ruth J F Loos, Patrik K E Magnusson, Nicholas G Martin, Grant W Montgomery, Kari E North, Nancy L Pedersen, Timothy D Spector, Elizabeth K Speliotes, Michael E Goddard, Jian Yang & Peter M Visscher
doi:10.1038/ng.3401
Matthew Robinson and colleagues report an analysis of population genetic differences in human height and body mass index (BMI) across 14 European populations. They estimate the proportion of additive genetic variance attributable to population genetic differences and find evidence for selection increasing height while reducing BMI in European nations. | | | | Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families pp1363 - 1369
Nadia Akawi, Jeremy McRae, Morad Ansari, Meena Balasubramanian, Moira Blyth, Angela F Brady, Stephen Clayton, Trevor Cole, Charu Deshpande, Tomas W Fitzgerald, Nicola Foulds, Richard Francis, George Gabriel, Sebastian S Gerety, Judith Goodship, Emma Hobson, Wendy D Jones, Shelagh Joss, Daniel King, Nikolai Klena, Ajith Kumar, Melissa Lees, Chris Lelliott, Jenny Lord, Dominic McMullan, Mary O'Regan, Deborah Osio, Virginia Piombo, Elena Prigmore, Diana Rajan, Elisabeth Rosser, Alejandro Sifrim, Audrey Smith, Ganesh J Swaminathan, Peter Turnpenny, James Whitworth, Caroline F Wright, Helen V Firth, Jeffrey C Barrett, Cecilia W Lo, David R FitzPatrick, Matthew E Hurles & the DDD study
doi:10.1038/ng.3410
Matthew Hurles, David FitzPatrick and colleagues report the discovery of four novel Mendelian disorders based on their analysis of exome sequence data from 4,125 families with diverse rare developmental disorders. They present their analytical pipeline as a general strategy for the discovery of genetic causes of autosomal recessive disorders.
See also: News and Views by Vissers & Veltman | Brief Communication by Guimier et al. | | | Top | |  | | Advertisement | | Primers in your inbox
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